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Django app for syncing and storing human genome reference data

Project description

=============================
Django Genome
=============================

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:alt: Python 3

Django app for syncing and storing human genome reference data

Documentation
-------------

The full documentation is at https://django-genome.readthedocs.io.

Quickstart
----------

Install Django Genome::

pip install django-genome

Add it to your `INSTALLED_APPS` (along with DRF and django-filters):

.. code-block:: python

INSTALLED_APPS = (
...
'rest_framework',
'django_filters',
...
'genome',
...
)

Add Django Genome's URL patterns:

.. code-block:: python

from genome import urls as genome_urls


urlpatterns = [
...
url(r'^', include(genome_urls, namespace='genome')),
...
]

Initial sync for genome models::

python manage.py genome_sync

Features
--------

* Includes models for Genome, Chromosome, CytoBand, Gene, Transcript, and Exons
* Syncs data for hg18, hg19, hg38 from HGNC and UCSC

Running Tests
-------------

Does the code actually work?

::

source <YOURVIRTUALENV>/bin/activate
(myenv) $ pip install tox
(myenv) $ tox

Credits
-------

Tools used in rendering this package:

* Cookiecutter_
* `cookiecutter-djangopackage`_

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`cookiecutter-djangopackage`: https://github.com/pydanny/cookiecutter-djangopackage




History
-------

0.1.0 (2017-12-30)
++++++++++++++++++

* First release on PyPI.
* Initial models and REST API
* Syncs data from HGNC and UCSC to build database

0.2.0 (2018-01-05)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.1.0...v0.2.0>`_

* Improved REST API Filters
* made Chromosomes and Gene Symbols save as uppercase to maintain consistency


0.2.1 (2018-01-08)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.2.0...v0.2.1>`_

* Fixed issues with migrations

0.2.2 (2018-01-12)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.2.1...v0.2.2>`_

* Fixed route names for SimpleRouter

0.3.0 (2018-02-09)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.2.2...v0.3.0>`_

* Updated requirements to the latest


0.4.0 (2018-03-30)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.3.0...v0.4.0>`_

* Added API for chromosomes
* Changed gene_symbol from being unique

0.5.0 (2018-04-04)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.4.0...v0.5.0>`_

* Added GraphQL Nodes

0.6.0 (2018-04-07)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.5.0...v0.6.0>`_

* Added support for Django 2 and Python 3.6
* Dropped support for Django < 1.11 and Python 2.7, 3.3, 3.4

0.6.1 (2018-04-18)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.0...v0.6.1>`_

* Updated 3rd party libs

0.6.2 (2018-05-14)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.1...v0.6.2>`_

* Updated chromosomes sync to ensure lexicographic ordering of chromosomes

0.6.3 (2018-05-16)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.2...v0.6.3>`_

* Updated sync to be able to skip sync of exons

0.6.4 (2018-05-16)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.3...v0.6.4>`_

* Updated setup.py to read requirements.txt

0.7.0 (2018-06-01)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.4...v0.7.0>`_

* Added Gene List model
* Removed support for GraphQL - this is not needed here. Applications that import this package can set up Nodes/Schema using models

0.7.1 (2018-06-07)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.7.0...v0.7.1>`_

* #54 - Updated management methods to allow for updating when retrieving latest changes from RefSeq
* #56 - Updated Gene model to have property ensembl_gene_id - which will check HGNC and Ensembl provided gene Ids

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